You do not say if this is an old mill that has just developed a fault , or a new mill you have just set up.
The fact that you can send the table out X inches and bring it back to zero makes no difference to Mach 3, since any faults will be cancelled out in the return.
What you should do is move right 1/2 inch, to take up any backlash, set up a DTI then send the machine 1 inch to the right and see what that distance is. If it is incorrect, send the machine another inch to the right and check that. If the fault over 2 inches is double the fault over one inch, then your steps per unit are not correct. You can carry on checking up to the extent of your DTI or calipers.